title: Genomic analysis of pandemic and post-pandemic influenza A pH1N1 viruses isolated in Rio Grande do Sul, Brazil.
abstract: During the 2009 influenza A pH1N1 pandemics in Brazil, the state that was most affected was Rio Grande do Sul (RS), with over 3,000 confirmed cases, including 298 deaths. While no cases were confirmed in 2010, 103 infections with 14 deaths by pH1N1 were reported in 2011. Genomic analysis of the circulating viruses is fundamental for understanding viral evolution and supporting vaccine development against these pathogens. This study investigated whole genomes of six pH1N1 virus isolates from pandemic and post-pandemic periods in RS, Brazil. Phylogenetic analysis using the concatenated genome segments demonstrated that at least two lineages of the virus co-circulated in RS during the 2009 pandemic period. Moreover, our analysis showed that the post-pandemic pH1N1 virus from 2011 constitutes a distinct clade whose ancestor belongs to clade 7. All six isolates contained amino acid substitutions in their proteins when compared to the archetype strains California/04/2009 and California/07/2009. The 2011 isolates contained more amino acid substitutions, and most of their genes were under purifying selection. Based on the amino acid substitutions in HA epitopes from strains isolated in RS, Brazil, in silico analysis predicted a decrease in vaccine efficacy against post-pandemic strains (median 31.562 %) in relation to pandemic ones (median 39.735 %).
authors.affiliation: Graduate Program in Pathology, Laboratory of Molecular Microbiology and Laboratory of Molecular Biology, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), R. Sarmento Leite, 245 / sala 309-Centro, Porto Alegre, RS, 90050-170, Brazil, fhsantanna@yahoo.com.br.
authors.forename: F H
authors.initials: FH
authors.lastname: Sant'Anna
authors.forename: L G A
authors.initials: LG
authors.lastname: Borges
authors.forename: P R V
authors.initials: PR
authors.lastname: Fallavena
authors.forename: T S
authors.initials: TS
authors.lastname: Gregianini
authors.forename: F
authors.initials: F
authors.lastname: Matias
authors.forename: R A
authors.initials: RA
authors.lastname: Halpin
authors.forename: D
authors.initials: D
authors.lastname: Wentworth
authors.forename: P A
authors.initials: PA
authors.lastname: d'Azevedo
authors.forename: A B G
authors.initials: AB
authors.lastname: Veiga
mesh_terms: D019943:Amino Acid Substitution; D001938:Brazil; D016000:Cluster Analysis; D016679:Genome, Viral; D005838:Genotype; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics / Q000276:immunology; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics* / Q000276:immunology / Q000302:isolation & purification*; D007252:Influenza Vaccines / Q000276:immunology; D007251:Influenza, Human / Q000821:virology*; D008969:Molecular Sequence Data; D020125:Mutation, Missense; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: C543345:H1N1 virus hemagglutinin; D019267:Hemagglutinin Glycoproteins, Influenza Virus; D007252:Influenza Vaccines; D012367:RNA, Viral